Auto-sync: 19 files at 2025-12-31 00:57

checkpoints/exp_20251230_045133_gen100_20251230_045142.json

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+      "data": {
+        "generation": 30,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_0222ead9be00",
+      "time": 1767088294.2477825,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 31",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 31,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_5afd08a99e08",
+      "time": 1767088294.280935,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 32",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 32,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_41b71036826b",
+      "time": 1767088294.3171146,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 33",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 33,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_762195c51cb3",
+      "time": 1767088294.3493202,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 34",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 34,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_8dda54fc3fce",
+      "time": 1767088294.3841527,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 35",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 35,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_7e3418a4d6ef",
+      "time": 1767088294.7745612,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 36",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 36,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_7abe5a4305b7",
+      "time": 1767088294.811632,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 37",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 37,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_0d3cb05d9b77",
+      "time": 1767088294.8469203,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 38",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 38,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_d64531119e9f",
+      "time": 1767088294.8794928,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 39",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 39,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_082640dadd2c",
+      "time": 1767088294.9142807,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 40",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 40,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_97100d12fb1a",
+      "time": 1767088295.332837,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 41",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 41,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_7d7298a572e3",
+      "time": 1767088295.3672278,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 42",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 42,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_023508aa5c03",
+      "time": 1767088295.401897,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 43",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 43,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_6ab42ed38d50",
+      "time": 1767088295.4342785,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 44",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 44,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_993b7d014002",
+      "time": 1767088295.469942,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 45",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 45,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_cdc786bb5346",
+      "time": 1767088296.1586132,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 46",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 46,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_1c2d9007ebbb",
+      "time": 1767088296.193247,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 47",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 47,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_9041f09ca7f3",
+      "time": 1767088296.2280078,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 48",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 48,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_6b7aef8bf311",
+      "time": 1767088296.2645051,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 49",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 49,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    },
+    {
+      "id": "evt_5897f42982ec",
+      "time": 1767088296.3007271,
+      "type": "generation",
+      "icon": "\ud83d\udd04",
+      "title": "Gen 50",
+      "detail": "pop=50 | best=1.0000",
+      "data": {
+        "generation": 50,
+        "population_size": 50,
+        "num_species": 1,
+        "best_fitness": 1.0,
+        "avg_fitness": 0.04,
+        "min_fitness": 0.0,
+        "max_fitness": 1.0,
+        "species_sizes": [
+          50
+        ]
+      }
+    }
+  ]
+}

checkpoints/test_run_gen10_20251230_043518.json

@@ -0,0 +1,78 @@
+{
+  "metadata": {
+    "name": "test_run",
+    "version": "v0.0.1",
+    "timestamp": "20251230_043518",
+    "generation": 10,
+    "best_fitness": 0.8,
+    "avg_fitness": 0.75,
+    "num_species": 2,
+    "population_size": 2,
+    "config_hash": "1afbf37d",
+    "notes": "Test checkpoint"
+  },
+  "config": {
+    "test": true,
+    "version": "1.0"
+  },
+  "population_traits": [
+    {
+      "traits": {
+        "a": 0.5,
+        "b": 0.3
+      },
+      "fitness": 0.7
+    },
+    {
+      "traits": {
+        "a": 0.6,
+        "b": 0.4
+      },
+      "fitness": 0.8
+    }
+  ],
+  "history": [
+    {
+      "generation": 0,
+      "best_fitness": 0.5
+    },
+    {
+      "generation": 1,
+      "best_fitness": 0.53
+    },
+    {
+      "generation": 2,
+      "best_fitness": 0.56
+    },
+    {
+      "generation": 3,
+      "best_fitness": 0.59
+    },
+    {
+      "generation": 4,
+      "best_fitness": 0.62
+    },
+    {
+      "generation": 5,
+      "best_fitness": 0.65
+    },
+    {
+      "generation": 6,
+      "best_fitness": 0.6799999999999999
+    },
+    {
+      "generation": 7,
+      "best_fitness": 0.71
+    },
+    {
+      "generation": 8,
+      "best_fitness": 0.74
+    },
+    {
+      "generation": 9,
+      "best_fitness": 0.77
+    }
+  ],
+  "species_data": null,
+  "event_log": null
+}

config.json

@@ -0,0 +1,223 @@
+{
+  "pressure": {
+    "default_center": 0.5,
+    "default_radius": 0.25,
+    "default_compression": 1.0,
+    "envelopes": {
+      "loss": {
+        "center": 0.3,
+        "radius": 0.2,
+        "compression": 1.0
+      },
+      "fitness": {
+        "center": 0.7,
+        "radius": 0.2,
+        "compression": 1.0
+      },
+      "learning_rate": {
+        "center": 0.5,
+        "radius": 0.3,
+        "compression": 0.8
+      }
+    }
+  },
+  "vp_thresholds": {
+    "VP0": 0.25,
+    "VP1": 0.5,
+    "VP2": 0.75,
+    "VP3": 0.99,
+    "modularity_collapse": 0.3,
+    "organism_collapse": 500
+  },
+  "convergence": {
+    "mutation_rate": 0.1,
+    "noise_std": 0.05
+  },
+  "attractor": {
+    "max_iterations": 1000,
+    "tolerance": 1e-06,
+    "learning_rate": 0.01
+  },
+  "pulse": {
+    "rate": 1.0,
+    "intensity": 1.0,
+    "decay": 0.99
+  },
+  "population": {
+    "size": 8,
+    "dimensions": 10,
+    "trait_keys": [
+      "x0",
+      "x1",
+      "x2",
+      "x3",
+      "x4",
+      "x5",
+      "x6",
+      "x7",
+      "x8",
+      "x9"
+    ],
+    "use_brains": true
+  },
+  "evolution": {
+    "generations": 100,
+    "mutation_rate": 0.1,
+    "mutation_strength": 0.1,
+    "crossover_rate": 0.7,
+    "fitness_function": "communication",
+    "target_species": 5,
+    "log_interval": 10,
+    "mode": "hybrid"
+  },
+  "speciation": {
+    "genetic_distance_threshold": 0.35,
+    "max_stagnation": 50,
+    "elitism": 2,
+    "survival_threshold": 0.2,
+    "crossover_rate": 0.7,
+    "min_species_size": 3
+  },
+  "dbscan": {
+    "eps": null,
+    "min_samples": 3,
+    "eps_percentile": 0.7,
+    "scale_features": true
+  },
+  "fitness": {
+    "function": "communication",
+    "bounds_low": -5.12,
+    "bounds_high": 5.12,
+    "normalize": true,
+    "invert": true
+  },
+  "node": {
+    "mutation_rate": 0.1,
+    "mutation_strength": 0.2
+  },
+  "brain": {
+    "enabled": false,
+    "hidden_sizes": [
+      16,
+      16
+    ],
+    "activation": "tanh",
+    "mutation_rate": 0.1,
+    "mutation_strength": 0.3
+  },
+  "lora_brain": {
+    "enabled": true,
+    "base_model": "Qwen/Qwen2.5-VL-3B-Instruct",
+    "quantization": "4bit",
+    "lora_rank": 8,
+    "lora_alpha": 16,
+    "lora_dropout": 0.0,
+    "target_modules": ["q_proj", "v_proj"],
+    "hidden_dim": 2048,
+    "use_flash_attention": false,
+    "max_memory": null,
+    "offload_folder": null
+  },
+  "vlm": {
+    "min_pixels": 200704,
+    "max_pixels": 1003520,
+    "max_new_tokens": 150,
+    "code_dir": ".",
+    "tasks_per_eval": 3
+  },
+  "weight_evolution": {
+    "algorithm": "CMA_ES",
+    "sigma_init": 0.1,
+    "weight_decay": 0.0,
+    "fitness_shaping": true
+  },
+  "nlp_training": {
+    "enabled": true,
+    "vocab_size": 1500,
+    "embed_dim": 64,
+    "hidden_dim": 128,
+    "max_seq_len": 32,
+    "num_lstm_layers": 1,
+    "num_classes": 2,
+    "population_size": 16,
+    "sigma_init": 0.3,
+    "train_samples": 64,
+    "eval_samples": 32
+  },
+  "explorer": {
+    "log_dir": "data/logs",
+    "shared_state_path": "data/.shared_simulation_state.json",
+    "max_events": 10000,
+    "causation_thresholds": {
+      "temporal_window": 1.0,
+      "correlation_min": 0.7,
+      "direct_max_delay": 0.1
+    }
+  },
+  "checkpointing": {
+    "enabled": true,
+    "checkpoint_every": 50,
+    "keep_best": 5,
+    "keep_recent": 3,
+    "checkpoint_dir": "checkpoints"
+  },
+  "logging": {
+    "wandb_project": "key-evolution",
+    "wandb_entity": null,
+    "tensorboard_enabled": true,
+    "tensorboard_logdir": "runs/key",
+    "log_interval": 1,
+    "log_level": "INFO"
+  },
+  "performance": {
+    "batch_size": 5,
+    "tick_delay_ms": 20,
+    "parallel_fitness": true,
+    "num_workers": 4
+  },
+  "hf_sync": {
+    "enabled": true,
+    "dataset_name": null,
+    "sync_checkpoints": true,
+    "sync_logs": true,
+    "retry_attempts": 3,
+    "timeout_seconds": 30
+  },
+  "visualization": {
+    "umap_enabled": true,
+    "umap_n_neighbors": 15,
+    "umap_min_dist": 0.1,
+    "umap_n_jobs": 1,
+    "plot_every": 10,
+    "max_history_points": 500
+  },
+  "selection": {
+    "method": "tournament",
+    "tournament_size": 3,
+    "truncation_threshold": 0.5
+  },
+  "experiment": {
+    "name": "default",
+    "tags": [
+      "evolution",
+      "bbob"
+    ],
+    "seed": 42,
+    "deterministic": true
+  },
+  "camel": {
+    "enabled": true,
+    "task_type": "role_playing",
+    "assistant_role": "assistant",
+    "user_role": "instructor",
+    "max_turns": 10,
+    "tasks_per_eval": 3,
+    "task_categories": ["problem_solving", "analysis"],
+    "partner_selection": "random",
+    "task_prompt": "Collaborate to solve the given problem step by step.",
+    "with_task_specify": true,
+    "model_backend": "local",
+    "temperature": 0.7,
+    "top_p": 0.9
+  }
+}

logs/.gitkeep

@@ -0,0 +1,3 @@
+# This directory stores log files
+# - *.log - Pipe-delimited log files
+# - *.jsonl - JSON Lines event files

logs/comm_events.jsonl

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logs/speciation.jsonl

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+{"timestamp": 1767139039.1277683, "iso_time": "2025-12-31T00:57:19.127770", "event": "species_created", "generation": 0, "species_id": 0, "founding_node_id": "9ad6804a", "founding_traits": {"x0": 0.37454, "x1": 0.950714, "x2": 0.731994, "x3": 0.598658, "x4": 0.156019, "x5": 0.155995, "x6": 0.058084, "x7": 0.866176, "x8": 0.601115, "x9": 0.708073}}
+{"timestamp": 1767139039.1299894, "iso_time": "2025-12-31T00:57:19.129991", "event": "speciation_snapshot", "generation": 0, "total_population": 8, "num_species": 1, "species": [{"id": 0, "size": 8, "avg_fitness": 0.515, "best_fitness": 0.515, "age": 0, "stagnant_gens": 0}]}

manifest.json

@@ -0,0 +1,8 @@
+{
+  "pushed_at": "2025-12-31T00:57:22.275166",
+  "files": 19,
+  "dirs": [
+    "checkpoints",
+    "logs"
+  ]
+}